• Journal of Microbiology
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• 제35권1호
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• pp.15-20
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• 1997

Kinetic studies were done to elucidate the reaction mechanism of purine nucleoside phosphorylase (PNP) in Micrococcus Luteus. PNP catalyzes the reversible phosphorolysis of ribonucleosides to their respective base. The effect of alternative competing substrates suggested that a single enzyme was involved in binding to the active site for all purine nucleosides, inosine, deoxyiosine, guanosine, deoxyguanosine, adenosine and deoxyadenosine. Affinity studies showed that pentose moiety reduced the binding capacity and methylation of ring N-1 of inosine and guanosine had little effect on binding to bacterial enzyme, whereas these compounds did not bind to the mammalian enzymes. The initial velocity and product inhibition studies demonstrated that the predominant mechanism of reaction was an ordered bi, bi reaction. The nucleoside bound to the enzyme first, followed by phosphate. Ribose 1-phosphate was the first product to leave, followed by base.

• Bulletin of the Korean Chemical Society
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• 제1권3호
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• pp.105-109
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• 1980

A general spectroscopic method is described for studies on the complex formation between metal ions and ligands, and is applied to $Cu^{2+}$ and $Ca^{2+}$binding to glycosaminoglycans. The order of binding constants for both ions is heparin >dermatan sulfate >chondroitin sulfate. The electrostatic forces are shown to be the predominant factor in the interaction. The 2- to 3-fold higher affinity for $Cu^{2+}$ than for $Ca^{2+}$ is obtained for heparin and dermatan sulfate, but little difference for chondroitin sulfate. These results are explained as chelation of both carboxyl and sulfate groups to $Cu^{2+}$ in former cases. The difference of binding constants among glycosaminoglycans is related to proposed various biological functions of the biopolymers.

• Bulletin of the Korean Chemical Society
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• 제20권10호
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• pp.1129-1135
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• 1999

Free energy perturbation and molecular dynamics simulations were carried out to investigate the relative binding affinities of [17] ketonand (1) toward alkali metal cations in methanol. The binding affinities of 1 toward the alkali metal cations were calculated to be in the order Li+ > Na+ > K+ > Rb+ > Cs+, whereas our recent theoretically predicted and experimentally observed binding affinities for [18]starand (2) were in the order K+ > Rb+ > Cs+ > Na+ > Li+. The extremely different affinities of 1 and 2 toward smaller cations, Li + and Na+ , were explained in terms of the differences in their ability to change the conformation to accommodate cations of different sizes. The carbonyl groups constituting the central cavity of 1 can reorganize to form a cavity with the optimal M+ -O distance, even for the smallest Li+, without imposing serious strain on 1. The highest affinity of 1 for Li+ was predominantly due to the highest Coulombic attraction between the smallest Li+ and the carbonyl oxygens of 1.

• Genomics & Informatics
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• 제19권1호
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• pp.9.1-9.5
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• 2021

Mammalian olfactory receptors are a family of G protein-coupled receptors (GPCRs) that occupy a large part of the genome. In human genes, olfactory receptors account for more than 40% of all GPCRs. Several types of GPCR structures have been identified, but there is no single olfactory receptor whose structure has been determined experimentally to date. The aim of this study was to model the interactions between an olfactory receptor and its ligands at the molecular level to provide hints on the binding modes between the OR2W1 olfactory receptor and its agonists and inverse agonists. The results demonstrated the modes of ligand binding in a three-dimensional model of OR2W1 and showed a statistically significant difference in binding affinity to the olfactory receptor between agonists and inverse agonists.

• BMB Reports
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• 제40권5호
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• pp.832-838
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• 2007

A novel inhibitory protein against blood coagulation factor Va (FVa) was purified from muscle protein of granulated ark (Tegillarca granosa, order Arcoida, marine bivalvia) by consecutive FPLC method using anion exchange and gel permeation chromatography. In the results of ESI-QTOF tandem mass analysis and database research, it was revealed that the purified T. granosa anticoagulant protein (TGAP) has 7.7 kDa of molecular mass and its partial sequence, HTHLQRAPHPNALGYHGK, has a high identity (64%) with serine/threonine kinase derived from Rhodopirellula baltica (order Planctomycetales, marine bacteria). TGAP could potently prolong thrombin time (TT), corresponding to inhibition of thrombin (FIIa) formation. Specific factor inhibitory assay showed that TGAP inhibits FVa among the major components of prothrombinase complex. In vitro assay for direct-binding affinity using surface plasmon resonance (SPR) spectrometer indicated that TGAP could be directly bound with FVa. In addition, the binding affinity of FVa to FII was decreased by addition of TGAP in dose-dependant manner ($IC_{50}$ value = 77.9 nM). These results illustrated that TGAP might interact with a heavy chain of FVa ($FVa_H$) bound to FII in prothrombin complex. The present study elucidated that non-cytotoxic T. granosa anticoagulant protein (TGAP) bound to FVa can prolong blood coagulation time by inhibiting conversion of FII to FIIa in blood coagulation cascade. In addition, TGAP did not significantly (P < 0.05) show fibrinolytic activity and cytotoxicity on venous endothelial cell line (ECV 304).

• 대한화학회지
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• 제42권1호
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• pp.1-8
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• 1998

티아졸 고리를 포함하는 lexitroposin에서, DNA minor groove의 염기쌍과 결합하는 부분인 티아졸의 분자정전기전위를 ab initio계산을 통해 구하였으며 protonate된 티아졸의 두 가지 가능한 형태에 대해 MNDO 및 ab initio방법으로 기하학적 구조를 최적화 하였다. 최적화된 구조에 대해 6-31G및 6-31G* basis set을 사용하여 양성자 친화도를 구하였으며 아울러 티아졸의 양성자 친화도에 미치는 치환기 효과를 알아보기 위해 전자를 주는 기와 전자를 끄는 기를 치환시킨 여러 치환 치아졸에 대해 양성자 친화도를 조사하였다. 그 결과 티아졸의 질소 원자가 DNA minor groove 쪽으로 배향되고 전자를 주는 기가 치환될 때 양성자 친화도가 증가됨을 알 수 있었다.

• BMB Reports
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• 제39권1호
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• pp.55-60
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• 2006

We describe a phage display strategy, based on the differential resistance of proteins to denaturant-induced unfolding, that can be used to select protein variants with improved conformational stability. To test the efficiency of this strategy, wild-type and two stable variants of ${\alpha}_1$-antitrypsin (${\alpha}_1AT$) were fused to the gene III protein of M13 phage. These phages were incubated in unfolding solution containing denaturant (urea or guanidinium chloride), and then subjected to an unfavorable refolding procedure (dialysis at $37^{\circ}C$). Once the ${\alpha}_1AT$ moiety of the fusion protein had unfolded in the unfolding solution, in which the denaturant concentration was higher than the unfolding transition midpoint ($C_m$) of the ${\alpha}_1AT$ variant, around 20% of the phage retained binding affinity to anti-${\alpha}_1AT$ antibody due to a low refolding efficiency. Moreover, this affinity reduced to less than 5% when 10 mg/mL skimmed milk (a misfolding-promoting additive) was included during the unfolding/refolding procedure. In contrast, most binding affinity (>95%) remained if the ${\alpha}_1AT$ variant was stable enough to resist unfolding. Because this selection procedure does not affect the infectivity of M13, the method is expected to be generally applicable to the high-throughput screening of stable protein variants, when activity-based screening is not possible.

• 한국수산과학회지
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• 제50권2호
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• pp.169-174
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• 2017

Immunoglobulin M (IgM) was purified from olive flounder Paralichthys olivaceus sera using mannan-binding protein (MBP) and protein L affinity columns (designated as MBPIgM and ProLIgM, respectively). A monoclonal antibody (MAb) against olive flounder IgM was produced. The MBPIgM and ProLIgM had apparent molecular weights of 77, 73, and 28 kDa in SDS-PAGE. Nine hybridomas secreting MAbs against olive flounder IgM were established: five MAbs for MBPIgM (1, 2, 3, 4, and 5) and four for ProLIgM (6, 7, 8, and 9). Western blotting indicated that seven MAbs recognized heavy (H; MAbs 1, 2, 3, 4, 5, 6, and 7) chains and one recognized light (L; MAb 9) chains of IgM, while MAb 8 did not recognize IgM. The results of enzyme-linked immunosorbent assay (ELISA) with bovine serum albumin (BSA, antigen) and the nine MAbs revealed that the optical density (OD) values of sera differed significantly between BSA- and non-immunized fish, despite some sera from non-immunized fish with slight high OD values. These results suggest that the MAbs produced in this study reacted specifically with the IgM from olive flounder.

• Natural Product Sciences
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• 제15권1호
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• pp.27-31
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• 2009

The present study was performed to investigate the binding affinity of the ethanol extract from the leaves of Morus alba (EMA) and some EMA related plant materials (EMA-D, EMA-DM) for melanin-concentrating hormone-1 receptor (MCH-1) and also to examine the antagonistic effect of them for the recombinant MCH-1 receptor expressed in CHO cells. EMA, dichloromethane fraction (EMA-D) and EMA-DM exhibited high affinity for mammalian MCH receptor in receptor binding assays ($IC_{50}$ value: 2.3, 1.6 and $1.0{\mu}g/ml$, respectively). Other plant materials (MMA-D, MMA-DM) obtained from methanol extracts from the leaves of Morus alba (MMA) also exhibited high affinity for mammalian MCH receptor, even though the $IC_{50}$ values of them were lower than those of EMA-D and EMA-DM. In Chinese hamster ovary (CHO) cells expressing human MCH-1, EMA-DM and EMA-D significantly inhibited MCH-induced intracellular $Ca^{2+}$ increase ($IC_{50}$ values: 16.5 and $22.7{\mu}g/ml$, respectively). These results clearly indicate that the ethanol extract from the leaves of Morus alba (EMA) and some EMA related plant materials (EMA-D, EMA-DM) are novel selective MCH-1 receptor antagonist, respectively.

• Archives of Pharmacal Research
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• 제23권4호
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• pp.353-359
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• 2000

${\alpha}_2$-Adrenoceptor antagonists, which can enhance synaptic norepinephrine levels by blocking feedback inhibition processes, are potentially useful in the treatment of disease states such. as depression, memory impairment, impotence and sexual dysfunction. (10bS)-1,2,3,5,6,10b-Hexahydropyrrolo[2,1-a]isoquinoline oxalate (YSL-3S) was evaluated in several in vitro biological tests to establish its pharmacological profile of activities as an ${\alpha}_2$-adrenoceptor antagonist. Saturation binding assay revealed that$^{3}[H]$rauwolscine bound to the $\alpha$$_2$-adrenoceptors with a Kd value of 6.3$\pm$0.5 nM and a Bmax value of 25l$\pm$39 fmol/mg protein in rat cortical synaptic membranes. Competitive binding assay showed that YSL-3S inhibited the binding of$^3[H]$rauwolscine (1 nM) in a concentration-dependent manner with a Ki value of 98.2$\pm$12.1 nM while it did not inhibit the binding of [$^3$H]cytisine (1.25 nM) to neuronal nicotinic cholinergic receptors. The Ki values of yohimbine, clonidine and norepinephrine for $^3[H]$rauwolscine binding were 15.8$\pm$1.0, 40.1$\pm$5.9 and 40.0$\pm$11.5 nM, respectively. In addition, the binding affinity of YSL-3S for ${\alpha}_2$-adrenoceptors was higher than that of its antipode and the racemic mixture. The functional activity of YSL-3S at the presynaptic ${\alpha}_2$-adrenoceptors was assessed using the prostatic portion of the rat vas deferens. Clonidine inhibited field-stimulated contractions of the vas deference in a dose-dependent manner. The presence of YSL-3S or yohimbine caused a parallel, rightward the dose-response curve of clonidine in a dose-dependent manner, indicating an antagonistic action at the presynaptic ${\alpha}_2$-adrenoceptors. The $pA_2$values of yohimbine and YSL-3S were 7.66$\pm$0.13 and 6.64$\pm$0.18, respectively. The results indicate that YSL-3S acts as a competitive antagonist at presynaptic ${\alpha}_2$ -adrenoceptors with a potency approximately ten times lower than yohimbine, but is devoid of binding affinity for neuronal nicotinic cholinergic receptors.